Takes place a few years after the first Ghost In The Shell manga. The Major has been missing since then, and Ghost in the Shell 2 follows the mysterious Motoko Aramaki as she runs an investigation into an incident at an organ factory and its consequences. She's on the run to clean up the mess and save herself in the process. Meanwhile, the former members of section 9 investigate Motoko to find out who she really is.

If you found the first manga confusing, then this one will make your head spin. Most of it consists of hacking which is chock full of technobabble, and it also adds some esoteric elements to the mix. I had to read most pages multiple times just to figure out what's going on, and I'm still nonplussed by the ending.

Spoiler (mouse over to view)

The premise is that after Motoko merged with the Puppet Master they created multiple versions of themselves. This manga focuses on Motoko Aramaki aka Motoko 11, with other "iterations" making appearances towards the end.

It's so abstract that it's no wonder it never got an anime adaptation, although I recognized some plot elements from it in the Stand Alone Complex series. If you are a die hard fan give it a read, if nothing else for the beautiful art, otherwise stick to the original Ghost in the Shell manga and 1.5.